Humans Share Microbiomes With Their Dogs


You know you share genes with your biological parents and kids, but what about microbes? A new study finds that families share skin, tongue and gut microbes with each other… and their dogs.

The study shows how the people and pets you live with affect the microscopic bacteria, fungi and other creatures living all over your body.

Researchers from universities across the U.S. studied 17 families with heterosexual parents and children ranging from infants to 18-year-olds; 17 families with one or more dogs, but no children; 18 families with kids and dogs; and 18 couples with no children or dogs. Volunteers sent in Q-tip-like swabs that they had rubbed on their foreheads, the palms of their hands, the tops of their tongues and a smudge of their feces (really). Study volunteers also sent in swabs of their dogs’ paws, fur and tongues.

The researchers ran genetic analyses on the samples, looking for the genetic material of microbes. They found that family members had more similar microbes on all parts of their bodies than people from different families. Family members’ skin microbes were the most alike, demonstrating that people share microbes on the surfaces they touch, and from touching each other. The adults in the family shared the most microbes.

Parents also shared many microbes with their children, but only if the kids were older than three. Younger kids may have vastly different microbes than their older family members because they’re still developing, the researchers wrote in a paper they published April 16 in the journal eLIFE.

As for Rover, he seems to have a some interesting effects on his humans’ microbes. As with other family members, adults share more microbes with their own dogs than they do with other people’s dogs.

But the researchers also found that simply owning a dog seems to have an effect on overall microbe-sharing. Cohabiting couples shared more microbes with one another if they had a dog, compared with couples that didn’t have dogs. Dog owners also had more species in common with other dog owners than they did with puppy-less people.

Want to know about the little critters that live on Fido? Dogs have more diverse microbes living on their bodies than humans do, including groups of microbes normally associated with humans, plus microbes that live in soil and water. One of the major groups of bacteria that dog owners and their pets share is Betaproteobacteria, which appear on human skin and on dog tongues.

Abnormal gut bacteria linked to severe malnutrition


There’s more to malnutrition than poor diet. Two complementary studies suggest that microbes have an important role to play in both the onset and treatment of a poorly understood form of malnutrition called kwashiorkor.

Malnutrition, the leading cause of death among children worldwide, remains something of a puzzle. It is unclear, for instance, why some children are especially prone to becoming malnourished when siblings they live with appear to fare better.

Now Jeffrey Gordon at Washington University in St Louis, Missouri, and his colleagues have found that a child’s risk of malnutrition may come down to the microbes in his or her guts.

Working in southern Malawi, the team identified sets of identical and non-identical twins in which one child had kwashiorkor – thought to be caused by a lack of protein – and the other did not, despite the shared genetics and diet. Gordon’s team took faecal samples from three sets of twins and transplanted the samples into the guts of mice, which were then fed a typical nutrient-poor Malawian diet.

Mouse weight lossAll of the mice lost some weight. However, some lost significantly more weight, and more quickly, than others. Further investigation showed that these mice had all received a faecal sample from children with kwashiorkor.

The finding strongly hinted that the mice had picked up a kwashiorkor-like condition from the microbes within the faecal implant, so the researchers studied the rodents’ gut flora. They found higher than normal levels of bacteria associated with illnesses such as inflammatory bowel disease.

The results suggest pathogenic microbes may heighten the problems of malnutrition in some children, says Jeremy Nicholson at Imperial College London, a member of the study team. “There’s a lot of work revolving around obesogenesis – how given a standard diet one set of bugs might make more calories available than another set,” he says. “But the other side of that coin is that maybe particular bugs can restrict calorie availability and exacerbate a poor diet.”

Indi Trehan at Washington University, another member of the research team, agrees. “I think it is correct that there are more factors than simple food insecurity at play in terms of malnutrition,” he says.

Antibiotic aidTrehan is lead author on a second new study, which examines how children with kwashiorkor respond when given nutrient-rich therapeutic diets. Trehan’s team found that the children were significantly less likely to become malnourished once the dietary treatment had ended if they were given a course of antibiotics along with the diet.

Together, the studies help us understand the role that infections might play in malnutrition, says Trehan. This might point towards a future in which microbial concoctions can be tailored to guard against such infections and treat specific conditions, suggests Nicholson.

Alexander Khoruts at the University of Minnesota in Minneapolis has been using faecal transplants to treat resistant Clostridium difficile disease in humans. “It is likely that microbiota are involved in pathogenesis of many other diseases, and it is possible that faecal transplants may be an approach to treat those as well,” he says. But because gut bacteria are so complex, he thinks more research will be needed to develop appropriate microbe-based therapies.

Are Bacteria Making You Hungry?


Over the last half decade, it has become increasingly clear that the normal gastrointestinal (GI) bacteria play a variety of very important roles in the biology of human and animals. Now Vic Norris of the University of Rouen, France, and coauthors propose yet another role for GI bacteria: that they exert some control over their hosts’ appetites. Their review was published online ahead of print in the Journal of Bacteriology.

This hypothesis is based in large part on observations of the number of roles bacteria are already known to play in host biology, as well as their relationship to the host system. “Bacteria both recognize and synthesize neuroendocrine hormones,” Norris et al. write. “This has led to the hypothesis that microbes within the gut comprise a community that forms a microbial organ interfacing with the mammalian nervous system that innervates the gastrointestinal tract.” (That nervous system innervating the GI tract is called the “enteric nervous system.” It contains roughly half a billion neurons, compared with 85 billion neurons in the central nervous system.)

“The gut microbiota respond both to both the nutrients consumed by their hosts and to the state of their hosts as signaled by various hormones,” write Norris et al. That communication presumably goes both ways: they also generate compounds that are used for signaling within the human system, “including neurotransmitters such as GABA, amino acids such as tyrosine and tryptophan — which can be converted into the mood-determining molecules, dopamine and serotonin” — and much else, says Norris.

Furthermore, it is becoming increasingly clear that gut bacteria may play a role in diseases such as cancer, metabolic syndrome, and thyroid disease, through their influence on host signaling pathways. They may even influence mood disorders, according to recent, pioneering studies, via actions on dopamine and peptides involved in appetite. The gut bacterium, Campilobacter jejuni, has been implicated in the induction of anxiety in mice, says Norris.

But do the gut flora in fact use their abilities to influence choice of food? The investigators propose a variety of experiments that could help answer this question, including epidemiological studies, and “experiments correlating the presence of particular bacterial metabolites with images of the activity of regions of the brain associated with appetite and pleasure.”

1.V. Norris, F. Molina, A. T. Gewirtz. Hypothesis: bacteria control host appetites. Journal of Bacteriology, 2012; DOI: 10.1128/JB.01384-12

Genetically Engineered Stomach Microbe Converts Seaweed into Ethanol

Seaweed may well be an ideal plant to turn into biofuel. It grows in much of the two thirds of the planet that is underwater, so it wouldn’t crowd out food crops the way corn for ethanol does. Because it draws its own nutrients and water from the sea, it requires no fertilizer or irrigation. Most importantly for would-be biofuel-makers, it contains no lignin—a strong strand of complex sugars that stiffens plant stalks and poses a big obstacle to turning land-based plants such as switchgrass into biofuel.

Researchers at Bio Architecture Lab, Inc., (BAL) and the University of Washington in Seattle have now taken the first step to exploit the natural advantages of seaweed. They have built a microbe capable of digesting it and converting it into ethanol or other fuels or chemicals. Synthetic biologist Yasuo Yoshikuni, a co-founder of BAL, and his colleagues took Escherichia coli, a gut bacterium most famous as a food contaminant, and made some genetic modifications that give it the ability to turn the sugars in an edible kelp called kombu into fuel. They report their findings in the January 20 issue of the journal Science.

To get his E. coli to digest kombu, Yoshikuni turned to nature—specifically, he looked into the genetics of natural microbes that can break down alginate, the predominant sugar molecule in the brown seaweed. “The form of the sugar inside the seaweed is very exotic,” Yoshikuni told Scientific American. “There is no industrial microbe to break down alginate and convert it into fuels and chemical compounds.”

Once he and his colleagues had isolated the genes that would confer the required traits, they used a fosmid—a carrier for a small chunk of genetic code—to place the DNA into the E. coli cells, where it took its place in the microbe’s own genetic instruction set. To test the new genetically engineered bacterium, the researchers ground up some kombu, mixed it with water and added the altered E. coli. Before two days had gone by the solution contained about 5 percent ethanol and water. It also did this at (relatively) low temperatures between 25 and 30 degrees Celsius, both of which mean that the engineered microbe can turn seaweed to fuel without requiring the use of additional energy for the process.

An analysis from the Pacific Northwest National Laboratory (pdf) suggests that the U.S. could supply 1 percent of its annual gasoline needs by growing such seaweed for harvest in slightly less than 1 percent of the nation’s territorial waters. Humans already grow and harvest some 15 million metric tons of kombu and other seaweeds to eat. And there’s no reason to fear the newly engineered E. coli escaping into the wild and consuming the seaweed already out there, Yoshikuni argues. “E. coli loves the human gut, it doesn’t like the ocean environment,” he says. “I can hardly imagine it would do something. It would just be dead.”

The microbe could turn out to be useful for making molecules other than ethanol, such as isobutanol or even the precursors of plastics, Yoshikuni says. “Consider the microbe as the chassis with engineered functional modules,” or pathways to produce a specific molecule, Yoshikuni says. “If we integrate other pathways instead of the ethanol pathway, this microbe can be a platform for converting sugar into a variety of molecules.”

The fact that such a one-stop industrial microbe can turn seaweed into a variety of molecules has attracted the attention of outfits such as the U.S. Department of Energy’s Advanced Research Projects Agency–Energy, or ARPA–e, which has funded BAL work with DuPont to produce other molecules from such engineered microbes. “Because seaweed grows naturally in the ocean, it uses the two thirds of the planet that we don’t use for agriculture,” ARPA–e program director Jonathan Burbaum wrote in an e-mail. “ARPA–e is directing a small portion of the remaining funding toward an aquafarm experiment to measure area productivity and harvest efficiency.”

Common Bacteria Discovered to be Mind-Altering, Improving Mood and Reducing Anxiety

Hundreds of species of bacteria call the human gut their home. This gut “microbiome” influences our physiology and health in ways that scientists are only beginning to understand. Now, a new study suggests that gut bacteria can even mess with the mind, altering brain chemistry and changing mood and behavior.

John Cryan and colleagues at McMaster University in Canada fed mice a broth containing a benign bacterium, Lactobacillus rhamnosus. The scientists chose this particular bug partly because they had a handy supply and also because related Lactobacillus bacteria are a major ingredient of probiotic supplements and very little is known about their potential side effects, Cryan says.

In this case, the side effects appeared to be beneficial. Mice whose diets were supplemented with L. rhamnosus for 6 weeks exhibited fewer signs of stress and anxiety in standard lab tests, Cryan and colleagues reported yesterday in the Proceedings of the National Academy of Sciences.